Entropic trapping

Entropic trap A strategy aimed at improving the efficiency of catalytic antibodies, via the incorporation of a molecular constraint into the transition state analogue that gives the hapten a higher energy conformation than that of the reaction product. 

Han, J., Turner, S.W. and Craighead, H.G. (1999) Entropic trapping and escape of long DNA molecules at submicron size constriction. Phys. Rev. Lett., 83, 1688-1691. 

Han, 1., Craighead, H.G., Separation of long DNA molecules in a microfabricated entropic trap array. Science 2000, 288, 1026-1029. 

Dorfman, K.D., Brenner, H., Modeling DNA electrophoresis in microfluidic entropic trapping devices. Biomed. Microdevices 2002, 4(3), 237-244. 

A further improvement on the concept of using preassembled oligomers exploits the involvement of a template (covalent or noncovalent) to entropically trap the pieces... 

Anomalous migration data where the mobility decreases very rapidly with molecular size have been described by an entropic trapping of the molecules within the gel matrix. This effect should be noticeable when the pore size of the polymer matrix corresponds to the radius of gyration of the analyte. However, the electric forces reduce the entropic effect consequently it should contribute only at extremely low field strength. It does not seem relevant under normal CGE conditions, and cannot improve separations. 

Liu L, Li PS, Asher SA (1999) Entropic trapping of macromolecules by mesoscopic periodic voids in a polymer hydrogel. Nature 397(6715) 141-144... 

A nanofluidic channel device, consisting of many entropic traps, was designed and fabricated for the separation of long DNA molecules. The channel comprises narrow constrictions and wider regions that cause size-dependent trapping of DNA at the onset of a constriction. This process creates electrophoretic mobility differences, thus enabling efficient separation without the use of a gel matrix or PEF. Samples of long DNA molecules (5000-... 

When the radius of gyration exceeds the cavity size, the entropic trapping mechanism breaks down. For example, k-DNA was observed to move like an inchworm, simultaneously spanning multiple pores [34]. The DNA is not completely extended, however, since it can relax to fill the cavities due to a gain in entropy. 

Polymeric matrices formed from a colloidal template have also been used for DNA separations [22]. In contrast to the case in entropic trapping in this type of matrix [34], the electric field compresses the long A.-DNA into a single pore. As illustrated in Figure 54.13, at weak fields the DNA move slowly between the pores, with the direction of the motion biased by the electric field. As the field increases, rope-over-pulley dynamics are observed, whereas at the highest fields the DNA jumps across multiple pores and then coils up. This behavior can only be observed over limited stretches of the medium, since the DNA dynamics change sharply as it tries to transit from one domain to another at the boundaries [22],... 

The mobility dependence in Figure 54.14 can be explained qualitatively by a relatively simple model of the transport process [22]. At weak fields, the transport is dominated by entropic trapping, since the change in potential energy for moving in the field is not much greater than the decrease in entropy required to move between the cavities. As a result, the shorter DNA moves more quickly in... 

Rousseau, J., Drouin, G, and Slater, GW. Entropic trapping of DNA during gel electrophoresis effect of field Intensity and gel concentration, Phys. Rev. Lett., 79, 1945, 1997. 

This review gives an overview of current advances in nucleic acid separation by CE and microchip electrophoresis. The focus is on the separation mechanisms during CE, conventional separation matrices and thermoresponsive polymers solutions, UV and fluorescence detection, microchip-based CE, and entropic trapping networks. 

Fig. 4 Nanofluidic separation device with many entropic traps. A, Cross-sectional schematic diagram of the device. DNA molecules are trapped whenever they meet a thin region, because their Rg is much larger than the thin region depth. B, Top view of the device. Trapped DNA molecules eventually escape, with a probability of escape proportional to the length of the slit that the DNA molecule covers (Wj and Wb). Larger molecules have a higher escape probability because they cover wider regions of the slit (wb > Wa). Source From Separation of long DNA molecules in a microfabricated entropic trap array, in Science. ...

We hope that this brief review has given the reader a general feeling of the development and application of CE in the separation of nucleic acids. With the advent of capillary array electrophoresis and microchip electrophoresis, as well as remarkable improvements in separation matrices, CE has become a standardized and cost-effective technique in the separation of nucleic acids. Novel thermo-responsive polymer solutions combine the merits of different monomers, and offer the possibility to fine-tune the desirable properties of polymer molecular architecture and chemical composition. Artificial entropic trapping systems obviate the use of viscous polymer solutions, and even offer fast, unattended, miniaturized, and multiplexed platforms. Optimizing the geometry of these electrophoretic systems to both increase the separation and reduce the diffusion (band broadening) is the main topic for future research. 

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